def add_reaction(self, rxn: Reaction) -> None:
""" Add a Reaction object to the simulation. """
r_spec_list = None
p_spec_list = None
# Figure out if it's an iterable of reactants or a single reactant
try:
for r in rxn.reactants:
if isinstance(r, m.OrientedSpecies):
r_sym = self._species[r.spec.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, True, r.orient_num, r_spec_list)
else:
r_sym = self._species[r.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, False, 0, r_spec_list)
except TypeError:
r = rxn.reactants
if isinstance(r, m.OrientedSpecies):
r_sym = self._species[r.spec.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, True, r.orient_num, r_spec_list)
else:
r_sym = self._species[r.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, False, 0, r_spec_list)
try:
for p in rxn.products:
if isinstance(r, m.OrientedSpecies):
p_sym = self._species[p.spec.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, True, p.orient_num, p_spec_list)
else:
p_sym = self._species[p.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, False, 0, p_spec_list)
except TypeError:
p = rxn.products
if isinstance(r, m.OrientedSpecies):
p_sym = self._species[p.spec.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, True, p.orient_num, p_spec_list)
else:
p_sym = self._species[p.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, False, 0, p_spec_list)
logging.info("Add reaction '%s' to simulation" %
rxn.print_friendly_repr)
m.create_reaction(self._world,
r_spec_list,
p_spec_list,
rxn.rate_constant,
rxn.bkwd_rate_constant,
name=rxn.name)
mol_A = m.create_species(name="A", dc=1)
world.species_list.append(mol_A)
mol_B = m.create_species(name="B", dc=1)
world.species_list.append(mol_B)
mol_C = m.create_species(name="C", dc=1)
world.species_list.append(mol_C)
###
# Define reactions
###
# A + B -> C
rxn = m.create_reaction("%m + %m -> %m" % (mol_A, mol_B, mol_C),
name="rxn",
fwd_rate=10)
# Add to the world
world.rxn_list.append(rxn)
###
# Release molecules into box
###
list_of_mols_to_release = [mol_A, mol_B]
number_of_each_to_release = [100, 100]
world.release_mols(list_of_mols_to_release,
nrel=number_of_each_to_release,
loc="%o" % (box))
mol_A = m.create_species(name="A",dc=1)
world.species_list.append(mol_A)
mol_B = m.create_species(name="B",dc=1,type="SURFACE")
world.species_list.append(mol_B)
mol_C = m.create_species(name="C",dc=1)
world.species_list.append(mol_C)
###
# Define reactions
###
# A' + B' @ surf_reg_plane -> C,
rxn = m.create_reaction("%m + %m @ %r -> %m" % (mol_A, mol_B, surf_reg_plane, mol_C), name="rxn", fwd_rate = 10)
# Add to the world
world.rxn_list.append(rxn)
###
# Release molecules into box
###
list_of_mols_to_release = [mol_A]
number_of_each_to_release = [100]
world.release_mols(
list_of_mols_to_release,
nrel = number_of_each_to_release,
loc = [0.5,0,0])
mol_A = m.create_species(name="A", dc=1)
world.species_list.append(mol_A)
mol_B = m.create_species(name="B", dc=1)
world.species_list.append(mol_B)
mol_C = m.create_species(name="C", dc=1)
world.species_list.append(mol_C)
###
# Define reactions
###
# A -> 0
rxn_1 = m.create_reaction("%m -> 0" % (mol_A), name="rxn 1", fwd_rate=10)
# A -> B
rxn_2 = m.create_reaction("%m -> %m" % (mol_A, mol_B),
name="rxn 2",
fwd_rate=10)
# A + B -> C
rxn_3 = m.create_reaction("%m + %m -> %m" % (mol_A, mol_B, mol_C),
name="rxn 3",
fwd_rate=10)
# A + B <-> C
rxn_4 = m.create_reaction("%m + %m -> %m" % (mol_A, mol_B, mol_C),
name="rxn 4",
fwd_rate=10,
mol_A = m.create_species(name="A",dc=1)
world.species_list.append(mol_A)
mol_B = m.create_species(name="B",dc=1,type="SURFACE")
world.species_list.append(mol_B)
mol_C = m.create_species(name="C",dc=1,type="SURFACE")
world.species_list.append(mol_C)
###
# Define reactions
###
# A + B @ box[surf_reg] -> C
rxn_1 = m.create_reaction("%m; + %m; @ %o[%r] -> %m;" % (mol_A,mol_B,box,surf_reg,mol_C), name="rxn 1", fwd_rate = 10)
# Add to the world
world.rxn_list.append(rxn_1)
###
# Release molecules into the box
###
list_of_mols_to_release = [mol_A, mol_B]
number_of_each_to_release = [100, 100]
world.release_mols(list_of_mols_to_release,
nrel = number_of_each_to_release,
loc = ["%o" % (box), "%o[%r]" % (box, surf_reg)], orientations = ["",";"])
###
# Create pyMCell instance
world = m.mcell_create()
m.mcell_init_state(world)
dt = 1e-6
iterations = 300
m.mcell_set_time_step(world, dt)
m.mcell_set_iterations(world, iterations)
# Define one surface molecule and three volume molecules
vm1_sym = m.create_species(world, "vm1", 1e-6, False)
# vm1 -> NULL [1e5]
reactants2 = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
m.create_reaction(world, reactants2, None, 0.01, name="rxn")
# Create Scene for simulation
scene_name = "Scene"
scene = m.create_instance_object(world, scene_name)
# Create a spherical release site
pos_vec3 = m.Vector3()
diam_vec3 = m.Vector3(0.015, 0.015, 0.015)
position, diameter, sphere_release_object = m.create_release_site(
world, scene, pos_vec3, diam_vec3, m.SHAPE_SPHERICAL, 500, 0, vm1_sym,
"vm1_rel")
obj_name = "Torus"
mesh = m.create_polygon_object(world, torus.vert_list, torus.face_list,